Variant report

Variant	rs10192426
Chromosome Location	chr2:179966545-179966546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179965713..179967518-chr2:179989741..179992075,2	K562	blood:

Variant related genes	Relation type
ENSG00000238339	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10170520	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10174774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs10186198	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10205390	0.94[JPT][hapmap];0.88[YRI][hapmap]
rs10205999	0.83[AFR][1000 genomes]
rs10439299	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10930858	0.82[AFR][1000 genomes]
rs1158872	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11884516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11894870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11898291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12997314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs13026497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes]
rs13383965	0.83[EUR][1000 genomes]
rs13391602	0.85[EUR][1000 genomes]
rs13418701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1374378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1374379	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446674	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1979053	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4585064	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433757	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433761	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433764	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6734121	0.83[AFR][1000 genomes]
rs6736098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6742744	0.82[YRI][hapmap]
rs6743405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757681	0.90[YRI][hapmap]
rs7579536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes]
rs7608882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs873023	0.88[YRI][hapmap]
rs9288022	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10192426	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179961000-179970800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:179961200-179971200	Weak transcription	Dnd41	blood
3	chr2:179961600-179972400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:179961600-179972800	Weak transcription	Spleen	Spleen
5	chr2:179961600-179974000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:179961800-179972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:179962000-179972600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:179962000-179972800	Weak transcription	Fetal Thymus	thymus
9	chr2:179962400-179972600	Weak transcription	Left Ventricle	heart
10	chr2:179962800-179972400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:179963000-179970800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:179964200-179969600	Weak transcription	HMEC	breast
13	chr2:179964600-179967400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:179964800-179967800	Weak transcription	Adipose Nuclei	Adipose
15	chr2:179965000-179966600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr2:179965000-179967200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:179965200-179967400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:179965200-179969600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:179965200-179971400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:179965400-179969200	Weak transcription	Osteobl	bone
21	chr2:179965400-179970800	Weak transcription	HUVEC	blood vessel
22	chr2:179965400-179971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:179965600-179969800	Weak transcription	NHDF-Ad	bronchial
24	chr2:179966000-179967800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:179966000-179969200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:179966200-179969600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:179966200-179973000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:179966400-179968000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:179966400-179968600	Weak transcription	Fetal Lung	lung
30	chr2:179966400-179971000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:179966400-179972400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:179966400-179972600	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:179966400-179975600	Weak transcription	Aorta	Aorta

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